Merge pull request #3 from VemundFredriksen/integration-test-in-ci-pi…

…peline

Integration test in ci pipeline

.github/workflows/ci.yml

@@ -8,13 +8,32 @@ on:
   workflow_dispatch:
 
 jobs:
-    sonarcloud:
-        name: SonarCloud
+    test_and_analyze:
+        name: Test & Analyze
         runs-on: ubuntu-latest
         steps:
           - uses: actions/checkout@v3
             with:
               fetch-depth: 0 
+
+          - name: Set up Python
+            uses: actions/setup-python@v2
+            with:
+              python-version: '3.10'
+
+          - uses: actions/cache@v2
+            with:
+              path: ~/.cache/pip
+              key: ${{ hashFiles('setup.py') }}-${{ hashFiles('requirements.txt') }}
+
+          - name: Install dependencies
+            run: pip install -r requirements.txt
+
+          - name: Install tox
+            run: pip install tox
+          - name: Run tox
+            run: tox -e py
+
           - name: SonarCloud Scan
             uses: SonarSource/sonarcloud-github-action@master
             env:

.gitignore

@@ -3,4 +3,5 @@
 /out/*
 /synthlung.egg*/
 /build/*
-*__pycache__*
+*__pycache__*
+.coverage

requirements.txt

@@ -0,0 +1,6 @@
+numpy
+torch
+monai
+tqdm
+pytest
+pytest-cov

sonar-project.properties

@@ -1,6 +1,9 @@
 sonar.projectKey=VemundFredriksen_SynthLung
 sonar.organization=vemundfredriksen
 
+sonar.python.coverage.reportPaths=coverage.xml
+sonar.sources = synthlung/
+sonar.tests = tests/
 # This is the name and version displayed in the SonarCloud UI.
 #sonar.projectName=SynthLung
 #sonar.projectVersion=1.0

synthlung/utils/dataset_formatter.py

@@ -20,9 +20,9 @@ def generate_json(self) -> None:
         pass
 
 class MSDImageSourceFormatter(ImageSourceFormatter, JSONGenerator):
-    def __init__(self) -> None:
-        self.target_directory = "./assets/source/msd/"
-        self.source_directory = "./assets/Task06_Lung/"
+    def __init__(self, source_directory: str = "./assets/Task06_Lung/", target_directory: str = "./assets/source/msd/") -> None:
+        self.target_directory = target_directory
+        self.source_directory = source_directory
 
     def format(self) -> None:
         if not os.path.exists(self.target_directory):

tests/integration_tests/test_dataset_formatter.py

@@ -0,0 +1,72 @@
+import pytest
+from synthlung.utils.dataset_formatter import MSDImageSourceFormatter
+import shutil
+from pathlib import Path
+import json
+
+def test_msd_formatter_format():
+    # Arrange
+    source_dir = './tests/source'
+    target_dir = './tests/target'
+
+    shutil.os.makedirs(f'{source_dir}/imagesTr/')
+    shutil.os.makedirs(f'{source_dir}/labelsTr/')
+    dummy_images = ["lung_001.nii.gz", "lung_002.nii.gz", "lung_003.nii.gz"]
+    for image in dummy_images:
+        image_path = Path(f"{source_dir}/imagesTr/{image}")
+        label_path = Path(f"{source_dir}/labelsTr/{image}")
+        Path.touch(image_path)
+        Path.touch(label_path)
+
+
+    msd_image_source_formatter = MSDImageSourceFormatter(source_dir, target_dir)
+
+    # Act
+    msd_image_source_formatter.format()
+
+    # Assert
+    expected_files = ["source_msd_lung_001_image.nii.gz", "source_msd_lung_001_label.nii.gz", "source_msd_lung_002_image.nii.gz", "source_msd_lung_002_label.nii.gz", "source_msd_lung_003_image.nii.gz", "source_msd_lung_003_label.nii.gz"]
+    actual_files = sorted(shutil.os.listdir(target_dir))
+
+    assert expected_files == actual_files
+
+    # Cleanup
+    shutil.rmtree(source_dir)
+    shutil.rmtree(target_dir)
+
+def test_msd_formatter_generate_json():
+    # Arrange
+    target_dir = './tests/target/'
+    shutil.os.makedirs(target_dir)
+
+    dummy_images = ["source_msd_lung_001_image.nii.gz", "source_msd_lung_001_label.nii.gz", "source_msd_lung_002_image.nii.gz", "source_msd_lung_002_label.nii.gz"]
+    for image in dummy_images:
+        image_path = Path(f"{target_dir}/{image}")
+        Path.touch(image_path)
+
+
+    msd_image_source_formatter = MSDImageSourceFormatter(target_dir, target_dir)
+
+    # Act
+    msd_image_source_formatter.generate_json()
+
+    # Assert
+    expected_json = [
+        {
+            "image": f"{target_dir}source_msd_lung_001_image.nii.gz",
+            "label": f"{target_dir}source_msd_lung_001_label.nii.gz"
+        },
+        {
+            "image": f"{target_dir}source_msd_lung_002_image.nii.gz",
+            "label": f"{target_dir}source_msd_lung_002_label.nii.gz"
+        }
+    ]
+
+    actual_json = None
+    with open(f"{target_dir}/dataset.json", 'r') as json_file:
+        actual_json = json.load(json_file)
+
+    assert expected_json == actual_json
+
+    # Cleanup
+    shutil.rmtree(target_dir)

tox.ini

@@ -0,0 +1,14 @@
+[tox]
+envlist = py39
+skipsdist = True
+
+[testenv]
+deps =
+    pytest
+    pytest-cov
+commands = pytest --cov=synthlung --cov-report=xml --cov-config=tox.ini --cov-branch
+
+[coverage:run]
+relative_files = True
+source = synthlung/
+branch = True